[{"ddc":["570"],"date_created":"2023-04-27T09:41:48Z","year":"2024","publication":"Neuron","volume":112,"article_processing_charge":"Yes (via OA deal)","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"date_published":"2024-01-17T00:00:00Z","title":"Multipotent progenitors instruct ontogeny of the superior colliculus","quality_controlled":"1","type":"journal_article","oa_version":"Published Version","date_updated":"2025-05-14T09:39:37Z","file":[{"file_name":"2024_Neuron_Cheung.pdf","content_type":"application/pdf","date_updated":"2024-02-06T13:56:15Z","file_size":5942467,"access_level":"open_access","file_id":"14944","date_created":"2024-02-06T13:56:15Z","success":1,"checksum":"32b3788f7085cf44a84108d8faaff3ce","relation":"main_file","creator":"dernst"}],"department":[{"_id":"SiHi"},{"_id":"RySh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","last_name":"Cheung"},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Koppensteiner","first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948"},{"full_name":"Krausgruber, Thomas","first_name":"Thomas","last_name":"Krausgruber"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher"},{"last_name":"Schrammel","full_name":"Schrammel, Martin","id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d","first_name":"Martin"},{"first_name":"Natalie Y","id":"e68ece33-f6e0-11ea-865d-ae1031dcc090","full_name":"Özgen, Natalie Y","last_name":"Özgen"},{"full_name":"Ivec, Alexis","id":"1d144691-e8be-11ed-9b33-bdd3077fad4c","first_name":"Alexis","last_name":"Ivec"},{"last_name":"Bock","full_name":"Bock, Christoph","first_name":"Christoph"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"}],"oa":1,"_id":"12875","external_id":{"pmid":["38096816"]},"file_date_updated":"2024-02-06T13:56:15Z","scopus_import":"1","intvolume":"       112","page":"230-246.e11","article_type":"comment","language":[{"iso":"eng"}],"publisher":"Elsevier","related_material":{"link":[{"url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/","relation":"press_release","description":"News on ISTA Website"}]},"month":"01","publication_status":"published","acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","day":"17","pmid":1,"status":"public","publication_identifier":{"eisbn":["1234995621"],"issnl":["1234-5678"],"issn":["0896-6273"]},"issue":"2","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"doi":"10.1016/j.neuron.2023.11.009","abstract":[{"text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny.","lang":"eng"}]},{"date_created":"2024-01-14T23:00:56Z","ddc":["530"],"volume":15,"article_processing_charge":"Yes","publication":"Nature Communications","year":"2024","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","title":"Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium","date_published":"2024-01-02T00:00:00Z","researchdata_availability":"yes","project":[{"call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046"},{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated GermaNIum quanTum tEchnology","grant_number":"101069515"},{"_id":"bdc2ca30-d553-11ed-ba76-cf164a5bb811","grant_number":"101115315","name":"Quantum bits with Kitaev Transmons"},{"grant_number":"P32235","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF"},{"name":"Merging spin and superconducting qubits in planar Ge","grant_number":"P36507","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606","name":"Conventional and unconventional topological superconductors"}],"type":"journal_article","oa":1,"author":[{"last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","full_name":"Valentini, Marco","first_name":"Marco"},{"full_name":"Sagi, Oliver","first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","last_name":"Sagi"},{"last_name":"Baghumyan","full_name":"Baghumyan, Levon","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","first_name":"Levon"},{"last_name":"de Gijsel","id":"a0ece13c-b527-11ee-929d-bad130106eee","full_name":"de Gijsel, Thijs","first_name":"Thijs"},{"id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87","first_name":"Jason","full_name":"Jung, Jason","last_name":"Jung"},{"full_name":"Calcaterra, Stefano","first_name":"Stefano","last_name":"Calcaterra"},{"first_name":"Andrea","full_name":"Ballabio, Andrea","last_name":"Ballabio"},{"last_name":"Aguilera Servin","full_name":"Aguilera Servin, Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","first_name":"Juan L","orcid":"0000-0002-2862-8372"},{"orcid":"0000-0001-9985-9293","first_name":"Kushagra","full_name":"Aggarwal, Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","last_name":"Aggarwal"},{"first_name":"Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87","full_name":"Janik, Marian","last_name":"Janik"},{"last_name":"Adletzberger","full_name":"Adletzberger, Thomas","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"full_name":"Seoane Souto, Rubén","first_name":"Rubén","last_name":"Seoane Souto"},{"first_name":"Martin","full_name":"Leijnse, Martin","last_name":"Leijnse"},{"full_name":"Danon, Jeroen","first_name":"Jeroen","last_name":"Danon"},{"last_name":"Schrade","first_name":"Constantin","full_name":"Schrade, Constantin"},{"full_name":"Bakkers, Erik","first_name":"Erik","last_name":"Bakkers"},{"first_name":"Daniel","full_name":"Chrastina, Daniel","last_name":"Chrastina"},{"last_name":"Isella","first_name":"Giovanni","full_name":"Isella, Giovanni"},{"orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","last_name":"Katsaros"}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-023-44114-0\">https://doi.org/10.1038/s41467-023-44114-0</a>.","ama":"Valentini M, Sagi O, Baghumyan L, et al. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-023-44114-0\">10.1038/s41467-023-44114-0</a>","short":"M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.L. Aguilera Servin, K. Aggarwal, M. Janik, T. Adletzberger, R. Seoane Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024).","ieee":"M. Valentini <i>et al.</i>, “Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","mla":"Valentini, Marco, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” <i>Nature Communications</i>, vol. 15, 169, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-023-44114-0\">10.1038/s41467-023-44114-0</a>.","apa":"Valentini, M., Sagi, O., Baghumyan, L., de Gijsel, T., Jung, J., Calcaterra, S., … Katsaros, G. (2024). Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-44114-0\">https://doi.org/10.1038/s41467-023-44114-0</a>","ista":"Valentini M, Sagi O, Baghumyan L, de Gijsel T, Jung J, Calcaterra S, Ballabio A, Aguilera Servin JL, Aggarwal K, Janik M, Adletzberger T, Seoane Souto R, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. 2024. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. Nature Communications. 15, 169."},"department":[{"_id":"GeKa"}],"file":[{"file_id":"14825","date_created":"2024-01-17T11:03:00Z","success":1,"access_level":"open_access","date_updated":"2024-01-17T11:03:00Z","content_type":"application/pdf","file_size":2336595,"file_name":"2024_NatureComm_Valentini.pdf","creator":"dernst","checksum":"ef79173b45eeaf984ffa61ef2f8a52ab","relation":"main_file"}],"date_updated":"2026-02-26T11:39:00Z","oa_version":"Published Version","_id":"14793","scopus_import":"1","file_date_updated":"2024-01-17T11:03:00Z","external_id":{"oaworkID":["w4390499170"],"pmid":["38167818"]},"dataavailabilitystatement":"All experimental data included in this work are available at https://zenodo.org/records/10119346.","article_type":"original","intvolume":"        15","article_number":"169","oaworkID":1,"APC_amount":"12345","language":[{"iso":"eng"}],"supplementarymaterial":"yes","publisher":"Springer Nature","month":"01","ec_funded":1,"day":"02","publication_status":"published","acknowledgement":"We acknowledge Alexander Brinkmann, Alessandro Crippa, Francesco Giazotto, Andrew Higginbotham, Andrea Iorio, Giordano Scappucci, Christian Schonenberger, and Lukas Splitthoff for helpful discussions. We thank Marcel Verheijen for the support in the TEM analysis. This research and related results were made possible with the support of the NOMIS\r\nFoundation. It was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research andinnovation programme under Grant Agreement No 862046, the HORIZONRIA\r\n101069515 project, the European Innovation Council Pathfinder grant no. 101115315 (QuKiT), and the FWF Projects #P-32235, #P-36507 and #F-8606. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. R.S.S. acknowledges Spanish CM “Talento Program\"\r\nProject No. 2022-T1/IND-24070. J.J. acknowledges European Research Council TOCINA 834290.","publication_identifier":{"eissn":["2041-1723"]},"status":"public","pmid":1,"doi":"10.1038/s41467-023-44114-0","abstract":[{"text":"Superconductor/semiconductor hybrid devices have attracted increasing interest in the past years. Superconducting electronics aims to complement semiconductor technology, while hybrid architectures are at the forefront of new ideas such as topological superconductivity and protected qubits. In this work, we engineer the induced superconductivity in two-dimensional germanium hole gas by varying the distance between the quantum well and the aluminum. We demonstrate a hard superconducting gap and realize an electrically and flux tunable superconducting diode using a superconducting quantum interference device (SQUID). This allows to tune the current phase relation (CPR), to a regime where single Cooper pair tunneling is suppressed, creating a sin(2y) CPR. Shapiro experiments complement this interpretation and the microwave drive allows to create a diode with ≈ 100% efficiency. The reported results open up the path towards integration of spin qubit devices, microwave resonators and (protected) superconducting qubits on  the same silicon technology compatible platform.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}]},{"date_created":"2023-10-31T13:30:20Z","volume":34,"article_processing_charge":"No","publication":"Current Biology","year":"2024","main_file_link":[{"url":"https://doi.org/10.1101/2023.10.26.564092","open_access":"1"}],"quality_controlled":"1","date_published":"2024-02-26T00:00:00Z","title":"Fungal infection alters collective nutritional intake of ant colonies","researchdata_availability":"unclear","type":"journal_article","author":[{"last_name":"Csata","full_name":"Csata, Eniko","first_name":"Eniko"},{"full_name":"Perez-Escudero, Alfonso","first_name":"Alfonso","last_name":"Perez-Escudero"},{"last_name":"Laury","first_name":"Emmanuel","full_name":"Laury, Emmanuel"},{"last_name":"Leitner","full_name":"Leitner, Hanna","first_name":"Hanna","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7"},{"last_name":"Latil","first_name":"Gerard","full_name":"Latil, Gerard"},{"last_name":"Heinze","full_name":"Heinze, Juerge","first_name":"Juerge"},{"last_name":"Simpson","full_name":"Simpson, Stephen","first_name":"Stephen"},{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","last_name":"Cremer"},{"last_name":"Dussutour","full_name":"Dussutour, Audrey","first_name":"Audrey"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"E. Csata, A. Perez-Escudero, E. Laury, H. Leitner, G. Latil, J. Heinze, S. Simpson, S. Cremer, A. Dussutour, Current Biology 34 (2024) 902–909.e6.","ama":"Csata E, Perez-Escudero A, Laury E, et al. Fungal infection alters collective nutritional intake of ant colonies. <i>Current Biology</i>. 2024;34(4):902-909.e6. doi:<a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">10.1016/j.cub.2024.01.017</a>","chicago":"Csata, Eniko, Alfonso Perez-Escudero, Emmanuel Laury, Hanna Leitner, Gerard Latil, Juerge Heinze, Stephen Simpson, Sylvia Cremer, and Audrey Dussutour. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” <i>Current Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">https://doi.org/10.1016/j.cub.2024.01.017</a>.","ieee":"E. Csata <i>et al.</i>, “Fungal infection alters collective nutritional intake of ant colonies,” <i>Current Biology</i>, vol. 34, no. 4. Elsevier, p. 902–909.e6, 2024.","ista":"Csata E, Perez-Escudero A, Laury E, Leitner H, Latil G, Heinze J, Simpson S, Cremer S, Dussutour A. 2024. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 34(4), 902–909.e6.","mla":"Csata, Eniko, et al. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” <i>Current Biology</i>, vol. 34, no. 4, Elsevier, 2024, p. 902–909.e6, doi:<a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">10.1016/j.cub.2024.01.017</a>.","apa":"Csata, E., Perez-Escudero, A., Laury, E., Leitner, H., Latil, G., Heinze, J., … Dussutour, A. (2024). Fungal infection alters collective nutritional intake of ant colonies. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2024.01.017\">https://doi.org/10.1016/j.cub.2024.01.017</a>"},"department":[{"_id":"SyCr"}],"date_updated":"2026-03-18T11:15:21Z","oa_version":"Preprint","_id":"14479","scopus_import":"1","external_id":{"pmid":["38307022"]},"article_type":"original","dataavailabilitystatement":"no DAS","page":"902-909.e6","intvolume":"        34","language":[{"iso":"eng"}],"supplementarymaterial":"yes","publisher":"Elsevier","month":"02","day":"26","acknowledgement":"We are sincerely grateful to the referees for their valuable comments and suggestions, which helped us to improve the paper. We are thankful to Jorgen Eilenberg and Nicolai V. Meyling for the fungal strain, to Simon Tragust, Abel Bernadou, and Brian Lazarro for insightful discussions, to Iago Sanmartín-Villar, Léa Briard, Céline Maitrel, and Nolwenn Rissen for their help with the experiments. Furthermore, we thank Anna V. Grasse for help with the immune gene expression analyses. We thank Sergio Ibarra for creating the graphical abstract. E.C. was supported by a Fyssen Foundation grant and the Alexander von Humboldt Foundation. A.D. was supported by the CNRS.","publication_status":"published","publication_identifier":{"issnl":["1234-5678"],"eissn":["1879-0445"],"issn":["0960-9822"]},"status":"public","pmid":1,"abstract":[{"text":"In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6 Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12 but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16 How nutrition influences host-parasite interactions is not well understood, as studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23 We used the nutritional geometry framework24 to investigate the role of amino acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant, Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First, using 18 diets varying in AA:C composition, we established that the fungus performed best on the high-amino-acid diet 1:4. Second, we found that the fungus reached this optimal diet when given various diet pairings, revealing its ability to cope with nutritional challenges. Third, we showed that the optimal fungal diet reduced the lifespan of healthy ants when compared with a high-carbohydrate diet but had no effect on infected ants. Fourth, we revealed that infected ant colonies, given a choice between the optimal fungal diet and a high-carbohydrate diet, chose the optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling fungal infection from host immune response, we demonstrated that infected ants foraged on the optimal fungal diet in response to immune activation and not as a result of parasite manipulation. Therefore, we revealed that infected ant colonies chose a diet that is costly for survival in the long term but beneficial in the short term—a form of collective self-medication.","lang":"eng"}],"doi":"10.1016/j.cub.2024.01.017","issue":"4"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"ieee":"T. Graham, M. Kleshnina, and J. A. Filar, “Where do mistakes lead? A survey of games with incompetent players,” <i>Dynamic Games and Applications</i>, vol. 13. Springer Nature, pp. 231–264, 2023.","ama":"Graham T, Kleshnina M, Filar JA. Where do mistakes lead? A survey of games with incompetent players. <i>Dynamic Games and Applications</i>. 2023;13:231-264. doi:<a href=\"https://doi.org/10.1007/s13235-022-00425-3\">10.1007/s13235-022-00425-3</a>","short":"T. Graham, M. Kleshnina, J.A. Filar, Dynamic Games and Applications 13 (2023) 231–264.","chicago":"Graham, Thomas, Maria Kleshnina, and Jerzy A. Filar. “Where Do Mistakes Lead? A Survey of Games with Incompetent Players.” <i>Dynamic Games and Applications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s13235-022-00425-3\">https://doi.org/10.1007/s13235-022-00425-3</a>.","ista":"Graham T, Kleshnina M, Filar JA. 2023. Where do mistakes lead? A survey of games with incompetent players. Dynamic Games and Applications. 13, 231–264.","mla":"Graham, Thomas, et al. “Where Do Mistakes Lead? A Survey of Games with Incompetent Players.” <i>Dynamic Games and Applications</i>, vol. 13, Springer Nature, 2023, pp. 231–64, doi:<a href=\"https://doi.org/10.1007/s13235-022-00425-3\">10.1007/s13235-022-00425-3</a>.","apa":"Graham, T., Kleshnina, M., &#38; Filar, J. A. (2023). Where do mistakes lead? A survey of games with incompetent players. <i>Dynamic Games and Applications</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s13235-022-00425-3\">https://doi.org/10.1007/s13235-022-00425-3</a>"},"author":[{"last_name":"Graham","first_name":"Thomas","full_name":"Graham, Thomas"},{"full_name":"Kleshnina, Maria","first_name":"Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","last_name":"Kleshnina"},{"last_name":"Filar","full_name":"Filar, Jerzy A.","first_name":"Jerzy A."}],"oa":1,"date_updated":"2023-10-04T09:24:30Z","oa_version":"Published Version","department":[{"_id":"KrCh"}],"file":[{"relation":"main_file","checksum":"cd53b07e96f9030ddb348f305e5b58c7","creator":"dernst","access_level":"open_access","date_created":"2022-02-21T08:54:17Z","success":1,"file_id":"10781","file_name":"2022_DynamicGamesApplic_Graham.pdf","file_size":1890512,"content_type":"application/pdf","date_updated":"2022-02-21T08:54:17Z"}],"type":"journal_article","file_date_updated":"2022-02-21T08:54:17Z","scopus_import":"1","external_id":{"isi":["000753777100001"]},"_id":"10770","publication":"Dynamic Games and Applications","article_processing_charge":"No","volume":13,"year":"2023","ddc":["000"],"date_created":"2022-02-20T23:01:32Z","quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"title":"Where do mistakes lead? A survey of games with incompetent players","date_published":"2023-03-01T00:00:00Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","ec_funded":1,"acknowledgement":"The authors would like to acknowledge stimulating email discussions with Dr Wayne Lobb of W.A. Lobb LLC on the topic of evolutionary games. We also thank Dr Thomas Taimre for his input to the material in Sect. 3.\r\nThe authors would like to acknowledge partial support from the Australian Research Council under the Discovery grant DP180101602 and support by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411.","publication_status":"published","isi":1,"month":"03","doi":"10.1007/s13235-022-00425-3","abstract":[{"text":"Mathematical models often aim to describe a complicated mechanism in a cohesive and simple manner. However, reaching perfect balance between being simple enough or overly simplistic is a challenging task. Frequently, game-theoretic models have an underlying assumption that players, whenever they choose to execute a specific action, do so perfectly. In fact, it is rare that action execution perfectly coincides with intentions of individuals, giving rise to behavioural mistakes. The concept of incompetence of players was suggested to address this issue in game-theoretic settings. Under the assumption of incompetence, players have non-zero probabilities of executing a different strategy from the one they chose, leading to stochastic outcomes of the interactions. In this article, we survey results related to the concept of incompetence in classic as well as evolutionary game theory and provide several new results. We also suggest future extensions of the model and argue why it is important to take into account behavioural mistakes when analysing interactions among players in both economic and biological settings.","lang":"eng"}],"publication_identifier":{"issn":["2153-0785"],"eissn":["2153-0793"]},"status":"public","language":[{"iso":"eng"}],"article_type":"original","page":"231-264","intvolume":"        13","publisher":"Springer Nature"},{"day":"01","acknowledgement":"This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2018R1A5A1024958). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of Korea Meteorological Administration, and by the Korea Research Environment Open NETwork (KREONET), respectively. The authors declare no conflicts of interest.","publication_status":"published","related_material":{"link":[{"relation":"erratum","url":" https://doi.org/10.1007/s00382-022-06401-2"}]},"month":"01","isi":1,"abstract":[{"text":"The Indian summer monsoon rainfall (ISMR) has been declining since the 1950s. However, since 2002 it is reported to have revived. For these observed changes in the ISMR, several explanations have been reported. Among these explanations, however, the role of the eastern equatorial Indian Ocean (EEIO) is missing despite being one of the warmest regions in the Indian Ocean, and monotonously warming. A recent study reported that EEIO warming impacts the rainfall over northern India. Here we report that warming in the EEIO weakens the low-level Indian summer monsoon circulation and reduces ISMR. A warm EEIO drives easterly winds in the Indo–Pacific sector as a Gill response. The warm EEIO also enhances nocturnal convection offshore the western coast of Sumatra. The latent heating associated with the increased convection augments the Gill response and the resultant circulation opposes the monsoon low-level circulation and weakens the seasonal rainfall.","lang":"eng"}],"doi":"10.1007/s00382-022-06337-7","publication_identifier":{"issn":["0930-7575"],"eissn":["1432-0894"]},"status":"public","language":[{"iso":"eng"}],"page":"427-442","article_type":"original","intvolume":"        60","publisher":"Springer Nature","author":[{"last_name":"Goswami","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","first_name":"Bidyut B","full_name":"Goswami, Bidyut B"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"GOSWAMI BB. 2023. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 60, 427–442.","apa":"GOSWAMI, B. B. (2023). Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. <i>Climate Dynamics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00382-022-06337-7\">https://doi.org/10.1007/s00382-022-06337-7</a>","mla":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” <i>Climate Dynamics</i>, vol. 60, Springer Nature, 2023, pp. 427–42, doi:<a href=\"https://doi.org/10.1007/s00382-022-06337-7\">10.1007/s00382-022-06337-7</a>.","ieee":"B. B. GOSWAMI, “Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend,” <i>Climate Dynamics</i>, vol. 60. Springer Nature, pp. 427–442, 2023.","ama":"GOSWAMI BB. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. <i>Climate Dynamics</i>. 2023;60:427-442. doi:<a href=\"https://doi.org/10.1007/s00382-022-06337-7\">10.1007/s00382-022-06337-7</a>","short":"B.B. GOSWAMI, Climate Dynamics 60 (2023) 427–442.","chicago":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” <i>Climate Dynamics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00382-022-06337-7\">https://doi.org/10.1007/s00382-022-06337-7</a>."},"department":[{"_id":"CaMu"}],"oa_version":"None","date_updated":"2023-06-28T11:49:58Z","type":"journal_article","scopus_import":"1","external_id":{"isi":["000803119400002"]},"_id":"11434","volume":60,"article_processing_charge":"No","publication":"Climate Dynamics","year":"2023","date_created":"2022-06-05T22:01:50Z","quality_controlled":"1","title":"Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend","date_published":"2023-01-01T00:00:00Z"},{"language":[{"iso":"eng"}],"intvolume":"        16","page":"542-559","article_type":"original","publisher":"Wiley","publication_status":"published","acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","day":"01","month":"02","isi":1,"issue":"2","abstract":[{"lang":"eng","text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results."}],"doi":"10.1111/eva.13428","status":"public","publication_identifier":{"eissn":["1752-4571"]},"year":"2023","article_processing_charge":"No","volume":16,"publication":"Evolutionary Applications","date_created":"2022-07-03T22:01:33Z","ddc":["576"],"title":"Ten years of demographic modelling of divergence and speciation in the sea","date_published":"2023-02-01T00:00:00Z","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_id":"12685","success":1,"date_created":"2023-02-27T07:10:17Z","access_level":"open_access","date_updated":"2023-02-27T07:10:17Z","content_type":"application/pdf","file_size":2269822,"file_name":"2023_EvolutionaryApplications_DeJode.pdf","creator":"dernst","checksum":"d4d6fa9ddf36643af994a6a757919afb","relation":"main_file"}],"department":[{"_id":"NiBa"},{"_id":"BeVi"}],"date_updated":"2023-08-01T12:25:44Z","oa_version":"Published Version","oa":1,"author":[{"first_name":"Aurélien","full_name":"De Jode, Aurélien","last_name":"De Jode"},{"first_name":"Alan","full_name":"Le Moan, Alan","last_name":"Le Moan"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","first_name":"Sean"},{"orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","last_name":"Westram"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse"}],"has_accepted_license":"1","citation":{"chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” <i>Evolutionary Applications</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/eva.13428\">https://doi.org/10.1111/eva.13428</a>.","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. <i>Evolutionary Applications</i>. 2023;16(2):542-559. doi:<a href=\"https://doi.org/10.1111/eva.13428\">10.1111/eva.13428</a>","ieee":"A. De Jode <i>et al.</i>, “Ten years of demographic modelling of divergence and speciation in the sea,” <i>Evolutionary Applications</i>, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. <i>Evolutionary Applications</i>. Wiley. <a href=\"https://doi.org/10.1111/eva.13428\">https://doi.org/10.1111/eva.13428</a>","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” <i>Evolutionary Applications</i>, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:<a href=\"https://doi.org/10.1111/eva.13428\">10.1111/eva.13428</a>.","ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","external_id":{"isi":["000815663700001"]},"scopus_import":"1","file_date_updated":"2023-02-27T07:10:17Z","_id":"11479"},{"_id":"11706","file_date_updated":"2023-10-04T09:37:26Z","scopus_import":"1","external_id":{"isi":["000828530400001"]},"type":"journal_article","citation":{"short":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, J. Skokan, Random Structures and Algorithms 62 (2023) 1035–1055.","ama":"Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. Asymmetric Ramsey properties of random graphs involving cliques and cycles. <i>Random Structures and Algorithms</i>. 2023;62(4):1035-1055. doi:<a href=\"https://doi.org/10.1002/rsa.21106\">10.1002/rsa.21106</a>","chicago":"Liebenau, Anita, Letícia Mattos, Walner Mendonca dos Santos, and Jozef Skokan. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” <i>Random Structures and Algorithms</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/rsa.21106\">https://doi.org/10.1002/rsa.21106</a>.","ieee":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, and J. Skokan, “Asymmetric Ramsey properties of random graphs involving cliques and cycles,” <i>Random Structures and Algorithms</i>, vol. 62, no. 4. Wiley, pp. 1035–1055, 2023.","ista":"Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. 2023. Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. 62(4), 1035–1055.","mla":"Liebenau, Anita, et al. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” <i>Random Structures and Algorithms</i>, vol. 62, no. 4, Wiley, 2023, pp. 1035–55, doi:<a href=\"https://doi.org/10.1002/rsa.21106\">10.1002/rsa.21106</a>.","apa":"Liebenau, A., Mattos, L., Mendonca dos Santos, W., &#38; Skokan, J. (2023). Asymmetric Ramsey properties of random graphs involving cliques and cycles. <i>Random Structures and Algorithms</i>. Wiley. <a href=\"https://doi.org/10.1002/rsa.21106\">https://doi.org/10.1002/rsa.21106</a>"},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"full_name":"Liebenau, Anita","first_name":"Anita","last_name":"Liebenau"},{"last_name":"Mattos","full_name":"Mattos, Letícia","first_name":"Letícia"},{"id":"12c6bd4d-2cd0-11ec-a0da-e28f42f65ebd","first_name":"Walner","full_name":"Mendonca Dos Santos, Walner","last_name":"Mendonca Dos Santos"},{"first_name":"Jozef","full_name":"Skokan, Jozef","last_name":"Skokan"}],"date_updated":"2023-10-04T09:38:45Z","oa_version":"Published Version","file":[{"creator":"dernst","checksum":"3a5969d0c512aef01c30f3dc81c6d59b","relation":"main_file","content_type":"application/pdf","date_updated":"2023-10-04T09:37:26Z","file_size":1362334,"file_name":"2023_RandomStructureAlgorithms_Liebenau.pdf","file_id":"14389","date_created":"2023-10-04T09:37:26Z","success":1,"access_level":"open_access"}],"department":[{"_id":"MaKw"}],"tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"quality_controlled":"1","date_published":"2023-07-01T00:00:00Z","title":"Asymmetric Ramsey properties of random graphs involving cliques and cycles","ddc":["510"],"date_created":"2022-07-31T22:01:49Z","publication":"Random Structures and Algorithms","volume":62,"article_processing_charge":"Yes (in subscription journal)","year":"2023","publication_identifier":{"issn":["1042-9832"],"eissn":["1098-2418"]},"status":"public","abstract":[{"text":"We say that (Formula presented.) if, in every edge coloring (Formula presented.), we can find either a 1-colored copy of (Formula presented.) or a 2-colored copy of (Formula presented.). The well-known states that the threshold for the property (Formula presented.) is equal to (Formula presented.), where (Formula presented.) is given by (Formula presented.) for any pair of graphs (Formula presented.) and (Formula presented.) with (Formula presented.). In this article, we show the 0-statement of the Kohayakawa–Kreuter conjecture for every pair of cycles and cliques. ","lang":"eng"}],"doi":"10.1002/rsa.21106","issue":"4","isi":1,"month":"07","day":"01","publication_status":"published","acknowledgement":"This work was started at the thematic program GRAPHS@IMPA (January–March 2018), in Rio de Janeiro. We thank IMPA and the organisers for the hospitality and for providing a pleasant research environment. We thank Rob Morris for helpful discussions, and the anonymous referees for their careful reading and many helpful suggestions. Open Access funding enabled and organized by Projekt DEAL.\r\nA. Liebenau was supported by an ARC DECRA Fellowship Grant DE170100789. L. Mattos was supported by CAPES and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – The Berlin Mathematics Research Center MATH+ (EXC-2046/1, project ID: 390685689). W. Mendonça was supported by CAPES project 88882.332408/2010-01.","publisher":"Wiley","page":"1035-1055","article_type":"original","intvolume":"        62","language":[{"iso":"eng"}]},{"date_updated":"2023-08-14T12:48:09Z","oa_version":"Published Version","department":[{"_id":"LaEr"}],"file":[{"file_size":782278,"content_type":"application/pdf","date_updated":"2023-08-14T12:47:32Z","file_name":"2023_ProbabilityTheory_Cipolloni.pdf","date_created":"2023-08-14T12:47:32Z","success":1,"file_id":"14054","access_level":"open_access","creator":"dernst","relation":"main_file","checksum":"b9247827dae5544d1d19c37abe547abc"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"mla":"Cipolloni, Giorgio, et al. “Quenched Universality for Deformed Wigner Matrices.” <i>Probability Theory and Related Fields</i>, vol. 185, Springer Nature, 2023, pp. 1183–1218, doi:<a href=\"https://doi.org/10.1007/s00440-022-01156-7\">10.1007/s00440-022-01156-7</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2023). Quenched universality for deformed Wigner matrices. <i>Probability Theory and Related Fields</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00440-022-01156-7\">https://doi.org/10.1007/s00440-022-01156-7</a>","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 185, 1183–1218.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Quenched universality for deformed Wigner matrices,” <i>Probability Theory and Related Fields</i>, vol. 185. Springer Nature, pp. 1183–1218, 2023.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Quenched Universality for Deformed Wigner Matrices.” <i>Probability Theory and Related Fields</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00440-022-01156-7\">https://doi.org/10.1007/s00440-022-01156-7</a>.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields 185 (2023) 1183–1218.","ama":"Cipolloni G, Erdös L, Schröder DJ. Quenched universality for deformed Wigner matrices. <i>Probability Theory and Related Fields</i>. 2023;185:1183–1218. doi:<a href=\"https://doi.org/10.1007/s00440-022-01156-7\">10.1007/s00440-022-01156-7</a>"},"author":[{"full_name":"Cipolloni, Giorgio","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","last_name":"Cipolloni"},{"last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"last_name":"Schröder","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856"}],"oa":1,"type":"journal_article","external_id":{"isi":["000830344500001"],"arxiv":["2106.10200"]},"file_date_updated":"2023-08-14T12:47:32Z","scopus_import":"1","_id":"11741","year":"2023","publication":"Probability Theory and Related Fields","volume":185,"article_processing_charge":"Yes (via OA deal)","ddc":["510"],"date_created":"2022-08-07T22:02:00Z","title":"Quenched universality for deformed Wigner matrices","date_published":"2023-04-01T00:00:00Z","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"acknowledgement":"The authors are indebted to Sourav Chatterjee for forwarding the very inspiring question that Stephen Shenker originally addressed to him which initiated the current paper. They are also grateful that the authors of [23] kindly shared their preliminary numerical results in June 2021.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","publication_status":"published","day":"01","isi":1,"month":"04","abstract":[{"text":"Following E. Wigner’s original vision, we prove that sampling the eigenvalue gaps within the bulk spectrum of a fixed (deformed) Wigner matrix H yields the celebrated Wigner-Dyson-Mehta universal statistics with high probability. Similarly, we prove universality for a monoparametric family of deformed Wigner matrices H+xA with a deterministic Hermitian matrix A and a fixed Wigner matrix H, just using the randomness of a single scalar real random variable x. Both results constitute quenched versions of bulk universality that has so far only been proven in annealed sense with respect to the probability space of the matrix ensemble.","lang":"eng"}],"doi":"10.1007/s00440-022-01156-7","status":"public","publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]},"language":[{"iso":"eng"}],"arxiv":1,"intvolume":"       185","article_type":"original","page":"1183–1218","publisher":"Springer Nature"},{"quality_controlled":"1","title":"The Hasse principle for random Fano hypersurfaces","date_published":"2023-05-01T00:00:00Z","date_created":"2020-10-19T14:28:50Z","publication":"Annals of Mathematics","article_processing_charge":"No","volume":197,"year":"2023","main_file_link":[{"url":"https://arxiv.org/abs/2006.02356","open_access":"1"}],"_id":"8682","external_id":{"arxiv":["2006.02356"],"isi":["000966611000003"],"oaworkID":["w3033938593"]},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Browning, T. D., Boudec, P. L., &#38; Sawin, W. (2023). The Hasse principle for random Fano hypersurfaces. <i>Annals of Mathematics</i>. Princeton University. <a href=\"https://doi.org/10.4007/annals.2023.197.3.3\">https://doi.org/10.4007/annals.2023.197.3.3</a>","mla":"Browning, Timothy D., et al. “The Hasse Principle for Random Fano Hypersurfaces.” <i>Annals of Mathematics</i>, vol. 197, no. 3, Princeton University, 2023, pp. 1115–203, doi:<a href=\"https://doi.org/10.4007/annals.2023.197.3.3\">10.4007/annals.2023.197.3.3</a>.","ista":"Browning TD, Boudec PL, Sawin W. 2023. The Hasse principle for random Fano hypersurfaces. Annals of Mathematics. 197(3), 1115–1203.","ieee":"T. D. Browning, P. L. Boudec, and W. Sawin, “The Hasse principle for random Fano hypersurfaces,” <i>Annals of Mathematics</i>, vol. 197, no. 3. Princeton University, pp. 1115–1203, 2023.","chicago":"Browning, Timothy D, Pierre Le Boudec, and Will Sawin. “The Hasse Principle for Random Fano Hypersurfaces.” <i>Annals of Mathematics</i>. Princeton University, 2023. <a href=\"https://doi.org/10.4007/annals.2023.197.3.3\">https://doi.org/10.4007/annals.2023.197.3.3</a>.","short":"T.D. Browning, P.L. Boudec, W. Sawin, Annals of Mathematics 197 (2023) 1115–1203.","ama":"Browning TD, Boudec PL, Sawin W. The Hasse principle for random Fano hypersurfaces. <i>Annals of Mathematics</i>. 2023;197(3):1115-1203. doi:<a href=\"https://doi.org/10.4007/annals.2023.197.3.3\">10.4007/annals.2023.197.3.3</a>"},"author":[{"orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","last_name":"Browning"},{"last_name":"Boudec","full_name":"Boudec, Pierre Le","first_name":"Pierre Le"},{"full_name":"Sawin, Will","first_name":"Will","last_name":"Sawin"}],"oa":1,"date_updated":"2025-08-11T11:59:49Z","oa_version":"Preprint","department":[{"_id":"TiBr"}],"publisher":"Princeton University","article_type":"original","page":"1115-1203","oaworkID":1,"intvolume":"       197","language":[{"iso":"eng"}],"arxiv":1,"publication_identifier":{"issn":["0003-486X"]},"status":"public","abstract":[{"lang":"eng","text":"It is known that the Brauer--Manin obstruction to the Hasse principle is vacuous for smooth Fano hypersurfaces of dimension at least 3 over any number field. Moreover, for such varieties it follows from a general conjecture of Colliot-Thélène that the Brauer--Manin obstruction to the Hasse principle should be the only one, so that the Hasse principle is expected to hold. Working over the field of rational numbers and ordering Fano hypersurfaces of fixed degree and dimension by height, we prove that almost every such hypersurface satisfies the Hasse principle provided that the dimension is at least 3. This proves a conjecture of Poonen and Voloch in every case except for cubic surfaces."}],"doi":"10.4007/annals.2023.197.3.3","issue":"3","isi":1,"month":"05","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/when-is-necessary-sufficient/"}]},"day":"01","publication_status":"published"},{"publication_identifier":{"issn":["1369-5266"]},"pmid":1,"status":"public","abstract":[{"text":"To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling.","lang":"eng"}],"doi":"10.1016/j.pbi.2023.102443","issue":"10","month":"10","day":"01","publication_status":"published","acknowledgement":"The opening quote is not intended to reflect any political views of the authors. The authors by no means endorse the rhetoric of Donald Rumsfeld or the 2003 invasion of Iraq by the United States. Nevertheless, Rumsfeld's quote led to both public and academic debates on the concept of known and unknown unknowns, which can be applied to the recent unexpected developments in the auxin signaling field. We thank Linlin Qi and Huihuang Chen for their suggestions on figure presentation and inspiring discussions of TIR1/AFB signaling. Finally, we thank Aroosa Hussain for discussion of Greek mythology.","publisher":"Elsevier","article_type":"review","intvolume":"        75","article_number":"102443","language":[{"iso":"eng"}],"_id":"14313","scopus_import":"1","file_date_updated":"2023-11-02T17:03:20Z","external_id":{"pmid":["37666097"]},"type":"journal_article","author":[{"first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas","last_name":"Fiedler"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"}],"oa":1,"has_accepted_license":"1","citation":{"mla":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” <i>Current Opinion in Plant Biology</i>, vol. 75, no. 10, 102443, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">10.1016/j.pbi.2023.102443</a>.","apa":"Fiedler, L., &#38; Friml, J. (2023). Rapid auxin signaling: Unknowns old and new. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">https://doi.org/10.1016/j.pbi.2023.102443</a>","ista":"Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 75(10), 102443.","ieee":"L. Fiedler and J. Friml, “Rapid auxin signaling: Unknowns old and new,” <i>Current Opinion in Plant Biology</i>, vol. 75, no. 10. Elsevier, 2023.","chicago":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">https://doi.org/10.1016/j.pbi.2023.102443</a>.","short":"L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023).","ama":"Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. <i>Current Opinion in Plant Biology</i>. 2023;75(10). doi:<a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">10.1016/j.pbi.2023.102443</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"amally","relation":"main_file","checksum":"1c476c3414d2dfb0c85db0cb6cfd8a28","date_created":"2023-11-02T17:03:20Z","success":1,"file_id":"14482","access_level":"open_access","file_size":737872,"date_updated":"2023-11-02T17:03:20Z","content_type":"application/pdf","file_name":"Fiedler CurrOpinOlantBiol 2023_revised.pdf"}],"department":[{"_id":"JiFr"}],"oa_version":"Submitted Version","date_updated":"2023-11-07T08:17:13Z","quality_controlled":"1","date_published":"2023-10-01T00:00:00Z","title":"Rapid auxin signaling: Unknowns old and new","date_created":"2023-09-10T22:01:11Z","ddc":["580"],"volume":75,"article_processing_charge":"No","publication":"Current Opinion in Plant Biology","year":"2023"},{"year":"2023","publication":"Cell Reports","volume":42,"article_processing_charge":"Yes","ddc":["570"],"date_created":"2023-09-10T22:01:11Z","project":[{"name":"Inter-and intracellular signalling in schizophrenia","grant_number":"607616","call_identifier":"FP7","_id":"257BBB4C-B435-11E9-9278-68D0E5697425"}],"date_published":"2023-09-26T00:00:00Z","title":"Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","date_updated":"2023-09-15T07:14:12Z","department":[{"_id":"JoCs"}],"file":[{"file_size":4879455,"content_type":"application/pdf","date_updated":"2023-09-15T07:12:46Z","file_name":"2023_CellPress_Nardin.pdf","success":1,"date_created":"2023-09-15T07:12:46Z","file_id":"14337","access_level":"open_access","creator":"dernst","relation":"main_file","checksum":"ca77a304fb813c292550b8604b0fb41d"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">https://doi.org/10.1016/j.celrep.2023.113015</a>.","ama":"Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. <i>Cell Reports</i>. 2023;42(9). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">10.1016/j.celrep.2023.113015</a>","short":"M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).","ieee":"M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions,” <i>Cell Reports</i>, vol. 42, no. 9. Elsevier, 2023.","apa":"Nardin, M., Käfer, K., Stella, F., &#38; Csicsvari, J. L. (2023). Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">https://doi.org/10.1016/j.celrep.2023.113015</a>","mla":"Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” <i>Cell Reports</i>, vol. 42, no. 9, 113015, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">10.1016/j.celrep.2023.113015</a>.","ista":"Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9), 113015."},"has_accepted_license":"1","oa":1,"author":[{"last_name":"Nardin","first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570"},{"first_name":"Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","full_name":"Käfer, Karola","last_name":"Käfer"},{"id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","first_name":"Federico","full_name":"Stella, Federico","orcid":"0000-0001-9439-3148","last_name":"Stella"},{"last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","orcid":"0000-0002-5193-4036"}],"type":"journal_article","external_id":{"pmid":["37632747"]},"file_date_updated":"2023-09-15T07:12:46Z","scopus_import":"1","_id":"14314","language":[{"iso":"eng"}],"article_number":"113015","intvolume":"        42","article_type":"original","publisher":"Elsevier","acknowledgement":"We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS (grant 607616).","publication_status":"published","day":"26","ec_funded":1,"month":"09","issue":"9","abstract":[{"lang":"eng","text":"The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations."}],"doi":"10.1016/j.celrep.2023.113015","pmid":1,"status":"public","publication_identifier":{"eissn":["2211-1247"]}},{"publisher":"eLife Sciences Publications","article_type":"original","article_number":"RP89066","intvolume":"        12","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050-084X"]},"pmid":1,"status":"public","doi":"10.7554/eLife.89066","abstract":[{"lang":"eng","text":"During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels."}],"month":"09","day":"04","acknowledgement":"We thank the members of the Hetzer laboratory, Tony Hunter (Salk), Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital) for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin (Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH), and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC). This work was also supported by the Mass Spectrometry Core of the Salk Institute with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine. We thank Jolene Diedrich and Antonio Pinto for technical support.","publication_status":"published","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","date_published":"2023-09-04T00:00:00Z","title":"Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress","ddc":["570"],"date_created":"2023-09-10T22:01:11Z","publication":"eLife","article_processing_charge":"Yes","volume":12,"year":"2023","_id":"14315","file_date_updated":"2023-09-15T06:59:10Z","scopus_import":"1","external_id":{"pmid":["37665327"]},"type":"journal_article","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Cho, U. H., &#38; Hetzer, M. (2023). Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.89066\">https://doi.org/10.7554/eLife.89066</a>","mla":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” <i>ELife</i>, vol. 12, RP89066, eLife Sciences Publications, 2023, doi:<a href=\"https://doi.org/10.7554/eLife.89066\">10.7554/eLife.89066</a>.","ista":"Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.","ieee":"U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2023.","chicago":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” <i>ELife</i>. eLife Sciences Publications, 2023. <a href=\"https://doi.org/10.7554/eLife.89066\">https://doi.org/10.7554/eLife.89066</a>.","short":"U.H. Cho, M. Hetzer, ELife 12 (2023).","ama":"Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. <i>eLife</i>. 2023;12. doi:<a href=\"https://doi.org/10.7554/eLife.89066\">10.7554/eLife.89066</a>"},"author":[{"full_name":"Cho, Ukrae H.","first_name":"Ukrae H.","last_name":"Cho"},{"full_name":"Hetzer, Martin W","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","last_name":"Hetzer"}],"oa":1,"oa_version":"Published Version","date_updated":"2023-09-15T07:07:10Z","department":[{"_id":"MaHe"}],"file":[{"success":1,"date_created":"2023-09-15T06:59:10Z","file_id":"14336","access_level":"open_access","file_size":3703097,"date_updated":"2023-09-15T06:59:10Z","content_type":"application/pdf","file_name":"2023_eLife_Cho.pdf","creator":"dernst","relation":"main_file","checksum":"db24bf3d595507387b48d3799c33e289"}]},{"title":"Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway","date_published":"2023-09-01T00:00:00Z","quality_controlled":"1","date_created":"2023-09-10T22:01:12Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.03.27.534325"}],"year":"2023","publication":"Journal of Cell Science","article_processing_charge":"No","volume":136,"_id":"14316","external_id":{"pmid":["37539494"]},"scopus_import":"1","type":"journal_article","oa_version":"Preprint","date_updated":"2023-09-20T09:14:15Z","department":[{"_id":"DaSi"}],"citation":{"ieee":"M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J. Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway,” <i>Journal of Cell Science</i>, vol. 136, no. 17. The Company of Biologists, 2023.","chicago":"Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.261448\">https://doi.org/10.1242/jcs.261448</a>.","short":"M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Science 136 (2023).","ama":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. <i>Journal of Cell Science</i>. 2023;136(17). doi:<a href=\"https://doi.org/10.1242/jcs.261448\">10.1242/jcs.261448</a>","mla":"Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” <i>Journal of Cell Science</i>, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.261448\">10.1242/jcs.261448</a>.","apa":"Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., &#38; Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261448\">https://doi.org/10.1242/jcs.261448</a>","ista":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 136(17), jcs261448."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Nagano","full_name":"Nagano, Makoto","first_name":"Makoto"},{"first_name":"Kaito","full_name":"Aoshima, Kaito","last_name":"Aoshima"},{"last_name":"Shimamura","first_name":"Hiroki","full_name":"Shimamura, Hiroki"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","first_name":"Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus"},{"full_name":"Toshima, Junko Y.","first_name":"Junko Y.","last_name":"Toshima"},{"full_name":"Toshima, Jiro","first_name":"Jiro","last_name":"Toshima"}],"oa":1,"publisher":"The Company of Biologists","article_number":"jcs261448","intvolume":"       136","article_type":"original","language":[{"iso":"eng"}],"pmid":1,"status":"public","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"issue":"17","abstract":[{"text":"Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport. In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted to generate distinct transport vesicles at the trans-Golgi network (TGN), and the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories for these adaptors. Recently, we showed that vesicle transport from the TGN is crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However, these observations were incompatible with previous studies showing that these adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall mechanism responsible for regulation of Vps21p activity remains ambiguous. Here, we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and Ypt32p were found to have partially overlapping functions for recruitment of AP-1 and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors for Vps21p activation in the TGN–endosome trafficking pathway.","lang":"eng"}],"doi":"10.1242/jcs.261448","month":"09","publication_status":"published","day":"01"},{"file_date_updated":"2023-09-20T08:46:43Z","scopus_import":"1","_id":"14317","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution transformers: Affine invariant synthesis for safety objectives,” in <i>International Conference on Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 86–112.","chicago":"Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” In <i>International Conference on Computer Aided Verification</i>, 13966:86–112. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>.","short":"S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.","ama":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In: <i>International Conference on Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:86-112. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>","mla":"Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” <i>International Conference on Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 86–112, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>.","apa":"Akshay, S., Chatterjee, K., Meggendorfer, T., &#38; Zikelic, D. (2023). MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In <i>International Conference on Computer Aided Verification</i> (Vol. 13966, pp. 86–112). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>","ista":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 86–112."},"has_accepted_license":"1","author":[{"last_name":"Akshay","full_name":"Akshay, S.","first_name":"S."},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Tobias","full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","last_name":"Meggendorfer"},{"last_name":"Zikelic","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","orcid":"0000-0002-4681-1699"}],"oa":1,"oa_version":"Published Version","date_updated":"2025-07-14T09:09:56Z","file":[{"file_id":"14349","date_created":"2023-09-20T08:46:43Z","success":1,"access_level":"open_access","content_type":"application/pdf","date_updated":"2023-09-20T08:46:43Z","file_size":531745,"file_name":"2023_LNCS_Akshay.pdf","creator":"dernst","checksum":"f143c8eedf609f20f2aad2eeb496d53f","relation":"main_file"}],"department":[{"_id":"KrCh"}],"type":"conference","quality_controlled":"1","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"date_published":"2023-07-17T00:00:00Z","title":"MDPs as distribution transformers: Affine invariant synthesis for safety objectives","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"conference":{"name":"CAV: Computer Aided Verification","start_date":"2023-07-17","location":"Paris, France","end_date":"2023-07-22"},"publication":"International Conference on Computer Aided Verification","article_processing_charge":"Yes (in subscription journal)","volume":13966,"year":"2023","ddc":["000"],"date_created":"2023-09-10T22:01:12Z","abstract":[{"lang":"eng","text":"Markov decision processes can be viewed as transformers of probability distributions. While this view is useful from a practical standpoint to reason about trajectories of distributions, basic reachability and safety problems are known to be computationally intractable (i.e., Skolem-hard) to solve in such models. Further, we show that even for simple examples of MDPs, strategies for safety objectives over distributions can require infinite memory and randomization.\r\nIn light of this, we present a novel overapproximation approach to synthesize strategies in an MDP, such that a safety objective over the distributions is met. More precisely, we develop a new framework for template-based synthesis of certificates as affine distributional and inductive invariants for safety objectives in MDPs. We provide two algorithms within this framework. One can only synthesize memoryless strategies, but has relative completeness guarantees, while the other can synthesize general strategies. The runtime complexity of both algorithms is in PSPACE. We implement these algorithms and show that they can solve several non-trivial examples."}],"doi":"10.1007/978-3-031-37709-9_5","publication_identifier":{"isbn":["9783031377082"],"issn":["0302-9743"],"eissn":["1611-3349"]},"status":"public","day":"17","ec_funded":1,"acknowledgement":"This work was supported in part by the ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project EQuaVE and SERB Matrices grant MTR/2018/00074.","publication_status":"published","month":"07","alternative_title":["LNCS"],"publisher":"Springer Nature","language":[{"iso":"eng"}],"page":"86-112","intvolume":"     13966"},{"conference":{"name":"CAV: Computer Aided Verification","end_date":"2023-07-22","start_date":"2023-07-17","location":"Paris, France"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"date_published":"2023-07-17T00:00:00Z","title":"Automated tail bound analysis for probabilistic recurrence relations","quality_controlled":"1","ddc":["000"],"date_created":"2023-09-10T22:01:12Z","year":"2023","publication":"Computer Aided Verification","article_processing_charge":"Yes (in subscription journal)","volume":13966,"_id":"14318","file_date_updated":"2023-09-20T08:24:47Z","scopus_import":"1","type":"conference","oa_version":"Published Version","date_updated":"2025-07-14T09:09:57Z","file":[{"relation":"main_file","checksum":"42917e086f8c7699f3bccf84f74fe000","creator":"dernst","access_level":"open_access","success":1,"date_created":"2023-09-20T08:24:47Z","file_id":"14348","file_name":"2023_LNCS_Sun.pdf","file_size":624647,"date_updated":"2023-09-20T08:24:47Z","content_type":"application/pdf"}],"department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 16–39.","mla":"Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” <i>Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 16–39, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">10.1007/978-3-031-37709-9_2</a>.","apa":"Sun, Y., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2023). Automated tail bound analysis for probabilistic recurrence relations. In <i>Computer Aided Verification</i> (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">https://doi.org/10.1007/978-3-031-37709-9_2</a>","ama":"Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic recurrence relations. In: <i>Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:16-39. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">10.1007/978-3-031-37709-9_2</a>","short":"Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification, Springer Nature, 2023, pp. 16–39.","chicago":"Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In <i>Computer Aided Verification</i>, 13966:16–39. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">https://doi.org/10.1007/978-3-031-37709-9_2</a>.","ieee":"Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound analysis for probabilistic recurrence relations,” in <i>Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 16–39."},"has_accepted_license":"1","author":[{"last_name":"Sun","full_name":"Sun, Yican","first_name":"Yican"},{"full_name":"Fu, Hongfei","first_name":"Hongfei","last_name":"Fu"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar"}],"oa":1,"publisher":"Springer Nature","intvolume":"     13966","page":"16-39","language":[{"iso":"eng"}],"status":"public","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031377082"]},"abstract":[{"text":"Probabilistic recurrence relations (PRRs) are a standard formalism for describing the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem, the classical and most well-known approach is the cookbook method by Karp (JACM 1994), while other approaches are mostly limited to deriving tail bounds of specific PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing time and random passed sizes observe discrete or (piecewise) uniform distribution and whose recursive call is either a single procedure call or a divide-and-conquer. We first establish a theoretical approach via Markov’s inequality, and then instantiate the theoretical approach with a template-based algorithmic approach via a refined treatment of exponentiation. Experimental evaluation shows that our algorithmic approach is capable of deriving tail bounds that are (i) asymptotically tighter than Karp’s method, (ii) match the best-known manually-derived asymptotic tail bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor) than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover, our algorithmic approach handles all examples (including realistic PRRs such as QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing that our approach is efficient in practice.","lang":"eng"}],"doi":"10.1007/978-3-031-37709-9_2","alternative_title":["LNCS"],"related_material":{"link":[{"relation":"software","url":"https://github.com/boyvolcano/PRR"}]},"month":"07","publication_status":"published","acknowledgement":"We thank Prof. Bican Xia for valuable information on the exponential theory of reals. The work is partially supported by the National Natural Science Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt), the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.","day":"17","ec_funded":1},{"_id":"14319","external_id":{"arxiv":["2212.03100"]},"scopus_import":"1","file_date_updated":"2023-09-15T08:02:09Z","type":"journal_article","department":[{"_id":"MaKw"}],"file":[{"checksum":"52c46c8cb329f9aaee9ade01525f317b","relation":"main_file","creator":"dernst","file_name":"2023_elecJournCombinatorics_Anastos.pdf","date_updated":"2023-09-15T08:02:09Z","content_type":"application/pdf","file_size":247917,"access_level":"open_access","file_id":"14338","success":1,"date_created":"2023-09-15T08:02:09Z"}],"date_updated":"2023-09-15T08:12:30Z","oa_version":"Published Version","oa":1,"author":[{"first_name":"Michael","full_name":"Anastos, Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","last_name":"Anastos"},{"full_name":"Fabian, David","first_name":"David","last_name":"Fabian"},{"first_name":"Alp","full_name":"Müyesser, Alp","last_name":"Müyesser"},{"last_name":"Szabó","full_name":"Szabó, Tibor","first_name":"Tibor"}],"has_accepted_license":"1","citation":{"mla":"Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” <i>Electronic Journal of Combinatorics</i>, vol. 30, no. 3, P3.10, Electronic Journal of Combinatorics, 2023, doi:<a href=\"https://doi.org/10.37236/11714\">10.37236/11714</a>.","apa":"Anastos, M., Fabian, D., Müyesser, A., &#38; Szabó, T. (2023). Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/11714\">https://doi.org/10.37236/11714</a>","ista":"Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. 30(3), P3.10.","ieee":"M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets,” <i>Electronic Journal of Combinatorics</i>, vol. 30, no. 3. Electronic Journal of Combinatorics, 2023.","chicago":"Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2023. <a href=\"https://doi.org/10.37236/11714\">https://doi.org/10.37236/11714</a>.","ama":"Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. <i>Electronic Journal of Combinatorics</i>. 2023;30(3). doi:<a href=\"https://doi.org/10.37236/11714\">10.37236/11714</a>","short":"M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics 30 (2023)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"date_published":"2023-07-28T00:00:00Z","title":"Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"quality_controlled":"1","date_created":"2023-09-10T22:01:12Z","ddc":["510"],"year":"2023","volume":30,"article_processing_charge":"Yes","publication":"Electronic Journal of Combinatorics","status":"public","publication_identifier":{"eissn":["1077-8926"]},"issue":"3","license":"https://creativecommons.org/licenses/by-nd/4.0/","doi":"10.37236/11714","abstract":[{"lang":"eng","text":"We study multigraphs whose edge-sets are the union of three perfect matchings, M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6 n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2 f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture however that if G is bipartite, the same result holds with n - 2 replaced by n - 1. We give a construction that shows such a result would be tight. We\r\nalso make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities."}],"month":"07","publication_status":"published","acknowledgement":"Anastos has received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Sk lodowska-Curie grant agreement No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft (DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434).","ec_funded":1,"day":"28","publisher":"Electronic Journal of Combinatorics","intvolume":"        30","article_number":"P3.10","article_type":"original","language":[{"iso":"eng"}],"arxiv":1},{"title":"Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene","date_published":"2023-09-15T00:00:00Z","quality_controlled":"1","year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2210.06310"}],"publication":"Physical Review B","volume":108,"article_processing_charge":"No","date_created":"2023-09-12T07:12:12Z","external_id":{"arxiv":["2210.06310"]},"scopus_import":"1","_id":"14320","oa_version":"Preprint","date_updated":"2023-09-20T09:38:24Z","department":[{"_id":"MaSe"},{"_id":"ChLa"},{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. <i>Physical Review B</i>. 2023;108(12). doi:<a href=\"https://doi.org/10.1103/physrevb.108.125411\">10.1103/physrevb.108.125411</a>","short":"P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical Review B 108 (2023).","chicago":"Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young, and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevb.108.125411\">https://doi.org/10.1103/physrevb.108.125411</a>.","ieee":"P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn, “Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene,” <i>Physical Review B</i>, vol. 108, no. 12. American Physical Society, 2023.","ista":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. 108(12), 125411.","apa":"Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., &#38; Serbyn, M. (2023). Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.108.125411\">https://doi.org/10.1103/physrevb.108.125411</a>","mla":"Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” <i>Physical Review B</i>, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevb.108.125411\">10.1103/physrevb.108.125411</a>."},"oa":1,"author":[{"last_name":"Henderson","orcid":"0000-0002-5198-7445","first_name":"Paul M","full_name":"Henderson, Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425"},{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan"},{"last_name":"Zibrov","first_name":"Alexander A.","full_name":"Zibrov, Alexander A."},{"first_name":"Andrea F.","full_name":"Young, Andrea F.","last_name":"Young"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"}],"type":"journal_article","publisher":"American Physical Society","language":[{"iso":"eng"}],"arxiv":1,"article_number":"125411","intvolume":"       108","article_type":"original","issue":"12","abstract":[{"text":"The development of two-dimensional materials has resulted in a diverse range of novel, high-quality compounds with increasing complexity. A key requirement for a comprehensive quantitative theory is the accurate determination of these materials' band structure parameters. However, this task is challenging due to the intricate band structures and the indirect nature of experimental probes. In this work, we introduce a general framework to derive band structure parameters from experimental data using deep neural networks. We applied our method to the penetration field capacitance measurement of trilayer graphene, an effective probe of its density of states. First, we demonstrate that a trained deep network gives accurate predictions for the penetration field capacitance as a function of tight-binding parameters. Next, we use the fast and accurate predictions from the trained network to automatically determine tight-binding parameters directly from experimental data, with extracted parameters being in a good agreement with values in the literature. We conclude by discussing potential applications of our method to other materials and experimental techniques beyond penetration field capacitance.","lang":"eng"}],"doi":"10.1103/physrevb.108.125411","status":"public","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"publication_status":"published","acknowledgement":"A.F.Y. acknowledges primary support from the Department of Energy under award DE-SC0020043, and additional support from the Gordon and Betty Moore Foundation under award GBMF9471 for group operations.","day":"15","month":"09"},{"article_number":"104103","intvolume":"       159","article_type":"original","language":[{"iso":"eng"}],"arxiv":1,"publisher":"AIP Publishing","month":"09","publication_status":"published","acknowledgement":"We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan, and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot.","day":"11","ec_funded":1,"status":"public","pmid":1,"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"issue":"10","doi":"10.1063/5.0165806","abstract":[{"text":"We demonstrate the possibility of a coupling between the magnetization direction of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate the mechanism of the coupling, we analyze a minimal Stoner model that includes Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet. The proposed mechanism allows us to study magnetic anisotropy of the system with an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can change magnetocrystalline anisotropy of the substrate. Our research aims to motivate further experimental studies of the current-free chirality induced spin selectivity effect involving both enantiomers.","lang":"eng"}],"ddc":["530"],"date_created":"2023-09-13T09:25:09Z","year":"2023","publication":"The Journal of Chemical Physics","article_processing_charge":"Yes (in subscription journal)","volume":159,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"name":"Non-equilibrium Field Theory of Molecular Rotations","grant_number":"101062862","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338"},{"call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"}],"title":"Achiral dipoles on a ferromagnet can affect its magnetization direction","date_published":"2023-09-11T00:00:00Z","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"quality_controlled":"1","type":"journal_article","oa_version":"Published Version","date_updated":"2023-09-20T09:48:12Z","file":[{"access_level":"open_access","date_created":"2023-09-13T09:34:20Z","success":1,"file_id":"14322","file_name":"104103_1_5.0165806.pdf","file_size":5749653,"content_type":"application/pdf","date_updated":"2023-09-13T09:34:20Z","relation":"main_file","checksum":"507ab65ab29e2c987c94cabad7c5370b","creator":"acappell"}],"department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"ista":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 159(10), 104103.","mla":"Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” <i>The Journal of Chemical Physics</i>, vol. 159, no. 10, 104103, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0165806\">10.1063/5.0165806</a>.","apa":"Al Hyder, R., Cappellaro, A., Lemeshko, M., &#38; Volosniev, A. (2023). Achiral dipoles on a ferromagnet can affect its magnetization direction. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0165806\">https://doi.org/10.1063/5.0165806</a>","ieee":"R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles on a ferromagnet can affect its magnetization direction,” <i>The Journal of Chemical Physics</i>, vol. 159, no. 10. AIP Publishing, 2023.","ama":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet can affect its magnetization direction. <i>The Journal of Chemical Physics</i>. 2023;159(10). doi:<a href=\"https://doi.org/10.1063/5.0165806\">10.1063/5.0165806</a>","short":"R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical Physics 159 (2023).","chicago":"Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0165806\">https://doi.org/10.1063/5.0165806</a>."},"oa":1,"author":[{"id":"d1c405be-ae15-11ed-8510-ccf53278162e","first_name":"Ragheed","full_name":"Al Hyder, Ragheed","last_name":"Al Hyder"},{"last_name":"Cappellaro","first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","first_name":"Mikhail"},{"last_name":"Volosniev","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","full_name":"Volosniev, Artem"}],"_id":"14321","external_id":{"arxiv":["2306.17592"],"pmid":["37694742"]},"file_date_updated":"2023-09-13T09:34:20Z","scopus_import":"1"},{"file_date_updated":"2023-09-13T10:08:25Z","_id":"14323","author":[{"first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","full_name":"Kuzmicz-Kowalska, Katarzyna","last_name":"Kuzmicz-Kowalska"}],"has_accepted_license":"1","citation":{"ieee":"K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023.","chicago":"Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>.","short":"K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023.","ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>","mla":"Kuzmicz-Kowalska, Katarzyna. <i>Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>.","apa":"Kuzmicz-Kowalska, K. (2023). <i>Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>","ista":"Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"content_type":"application/pdf","date_updated":"2023-09-13T10:08:25Z","file_size":10147911,"file_name":"PhDThesis_KK_final_pdfA.pdf","embargo_to":"open_access","file_id":"14324","date_created":"2023-09-13T09:52:52Z","access_level":"closed","creator":"kkuzmicz","checksum":"bd83596869c814b24aeff7077d031c0e","relation":"main_file","embargo":"2025-03-13"},{"checksum":"aa2757ae4c3478041fd7e62c587d3e4d","relation":"source_file","creator":"kkuzmicz","file_name":"thesis_KK_final_corrections_092023.docx","date_updated":"2023-09-13T09:53:29Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":103980668,"access_level":"closed","file_id":"14325","date_created":"2023-09-13T09:53:29Z"}],"department":[{"_id":"GradSch"},{"_id":"AnKi"}],"date_updated":"2024-03-07T15:02:59Z","oa_version":"Published Version","type":"dissertation","date_published":"2023-09-13T00:00:00Z","title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","project":[{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"article_processing_charge":"No","year":"2023","date_created":"2023-09-13T10:07:18Z","ddc":["570"],"abstract":[{"text":"Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube.","lang":"eng"}],"doi":"10.15479/at:ista:14323","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","status":"public","day":"13","publication_status":"published","related_material":{"record":[{"status":"public","id":"7883","relation":"part_of_dissertation"}]},"month":"09","alternative_title":["ISTA Thesis"],"supervisor":[{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","first_name":"Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva"}],"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"page":"151"},{"article_number":"2307.09552","date_created":"2023-09-13T12:44:59Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2307.09552","open_access":"1"}],"year":"2023","publication":"arXiv","article_processing_charge":"No","arxiv":1,"language":[{"iso":"eng"}],"title":"Self-compatibility: Evaluating causal discovery without ground truth","date_published":"2023-07-18T00:00:00Z","type":"preprint","month":"07","publication_status":"submitted","date_updated":"2023-09-13T12:47:53Z","oa_version":"Preprint","department":[{"_id":"FrLo"}],"day":"18","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"P. M. Faller, L. C. Vankadara, A. A. Mastakouri, F. Locatello, and D. Janzing, “Self-compatibility: Evaluating causal discovery without ground truth,” <i>arXiv</i>. .","chicago":"Faller, Philipp M., Leena Chennuru Vankadara, Atalanti A. Mastakouri, Francesco Locatello, and Dominik Janzing. “Self-Compatibility: Evaluating Causal Discovery without Ground Truth.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2307.09552\">https://doi.org/10.48550/arXiv.2307.09552</a>.","short":"P.M. Faller, L.C. Vankadara, A.A. Mastakouri, F. Locatello, D. Janzing, ArXiv (n.d.).","ama":"Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2307.09552\">10.48550/arXiv.2307.09552</a>","mla":"Faller, Philipp M., et al. “Self-Compatibility: Evaluating Causal Discovery without Ground Truth.” <i>ArXiv</i>, 2307.09552, doi:<a href=\"https://doi.org/10.48550/arXiv.2307.09552\">10.48550/arXiv.2307.09552</a>.","apa":"Faller, P. M., Vankadara, L. C., Mastakouri, A. A., Locatello, F., &#38; Janzing, D. (n.d.). Self-compatibility: Evaluating causal discovery without ground truth. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2307.09552\">https://doi.org/10.48550/arXiv.2307.09552</a>","ista":"Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. arXiv, 2307.09552."},"author":[{"last_name":"Faller","first_name":"Philipp M.","full_name":"Faller, Philipp M."},{"last_name":"Vankadara","first_name":"Leena Chennuru","full_name":"Vankadara, Leena Chennuru"},{"full_name":"Mastakouri, Atalanti A.","first_name":"Atalanti A.","last_name":"Mastakouri"},{"orcid":"0000-0002-4850-0683","first_name":"Francesco","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"first_name":"Dominik","full_name":"Janzing, Dominik","last_name":"Janzing"}],"oa":1,"extern":"1","status":"public","_id":"14333","external_id":{"arxiv":["2307.09552"]},"doi":"10.48550/arXiv.2307.09552","abstract":[{"lang":"eng","text":"As causal ground truth is incredibly rare, causal discovery algorithms are\r\ncommonly only evaluated on simulated data. This is concerning, given that\r\nsimulations reflect common preconceptions about generating processes regarding\r\nnoise distributions, model classes, and more. In this work, we propose a novel\r\nmethod for falsifying the output of a causal discovery algorithm in the absence\r\nof ground truth. Our key insight is that while statistical learning seeks\r\nstability across subsets of data points, causal learning should seek stability\r\nacross subsets of variables. Motivated by this insight, our method relies on a\r\nnotion of compatibility between causal graphs learned on different subsets of\r\nvariables. We prove that detecting incompatibilities can falsify wrongly\r\ninferred causal relations due to violation of assumptions or errors from finite\r\nsample effects. Although passing such compatibility tests is only a necessary\r\ncriterion for good performance, we argue that it provides strong evidence for\r\nthe causal models whenever compatibility entails strong implications for the\r\njoint distribution. We also demonstrate experimentally that detection of\r\nincompatibilities can aid in causal model selection."}]}]